From 329a895fb82185a27fff7b842ed891700fa4e705 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 25 Jul 2024 12:07:17 -0400
Subject: [PATCH 01/15] add back labpdfproc command

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 90c9dca..68eef87 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,6 +42,9 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
+[project.scripts]
+labpdfproc = "diffpy.labpdfproc.labpdfprocapp:main"
+
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)

From 6954a2996010f30ea9444257c3bb438c5c5ac1de Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 25 Jul 2024 12:31:35 -0400
Subject: [PATCH 02/15] change default to fast cve, add brute-force option,
 handle muD out-of-range error

---
 src/diffpy/labpdfproc/labpdfprocapp.py | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index aedbd0a..9ebbbd7 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -1,6 +1,7 @@
 import sys
 from argparse import ArgumentParser
 
+from diffpy.labpdfproc.fast_cve import apply_fast_corr, fast_compute_cve
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
 from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
 from diffpy.utils.parsers.loaddata import loadData
@@ -72,6 +73,13 @@ def get_args(override_cli_inputs=None):
         action="store_true",
         help="Outputs will not overwrite existing file unless --force is specified.",
     )
+    p.add_argument(
+        "-b",
+        "--brute-force",
+        action="store_true",
+        help="The absorption correction will be computed using brute-force calculation "
+        "if this flag is set. Default is using fast calculation. ",
+    )
     p.add_argument(
         "-u",
         "--user-metadata",
@@ -134,11 +142,20 @@ def main():
             metadata=load_metadata(args, filepath),
         )
 
-        absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)
-        corrected_data = apply_corr(input_pattern, absorption_correction)
+        if args.brute_force:
+            absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)
+            corrected_data = apply_corr(input_pattern, absorption_correction)
+        else:
+            if args.mud > 6 or args.mud < 0.5:
+                sys.exit(
+                    "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
+                    "Please rerun with a value within this range or use -b enable brute-force calculation. "
+                )
+            absorption_correction = fast_compute_cve(input_pattern, args.mud, args.wavelength)
+            corrected_data = apply_fast_corr(input_pattern, absorption_correction)
+
         corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
         corrected_data.dump(f"{outfile}", xtype="tth")
-
         if args.output_correction:
             absorption_correction.dump(f"{corrfile}", xtype="tth")
 

From 97bcc00f4b82e8da024a9d014851a9a9c58f3aff Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 25 Jul 2024 12:35:20 -0400
Subject: [PATCH 03/15] minor correction on output correction command

---
 src/diffpy/labpdfproc/labpdfprocapp.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 9ebbbd7..c2fe16f 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -65,7 +65,6 @@ def get_args(override_cli_inputs=None):
         action="store_true",
         help="The absorption correction will be output to a file if this "
         "flag is set. Default is that it is not output.",
-        default="tth",
     )
     p.add_argument(
         "-f",

From 2487ae63f385a99b4c1d2daf6b8b36909e6020a0 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 25 Jul 2024 12:47:40 -0400
Subject: [PATCH 04/15] add brute force argument to metadata test

---
 src/diffpy/labpdfproc/tests/test_tools.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 3b4847f..fda91fb 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -312,6 +312,7 @@ def test_load_metadata(mocker, user_filesystem):
             "wavelength": 0.71,
             "output_directory": str(Path.cwd().resolve()),
             "xtype": "tth",
+            "brute_force": False,
             "key": "value",
             "username": "cli_username",
             "email": "cli@email.com",

From 7d0d57440221fc19c901a3131f59e20ea86ec695 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Fri, 26 Jul 2024 13:13:07 -0400
Subject: [PATCH 05/15] remove duplicated functions in fast cve

---
 src/diffpy/labpdfproc/fast_cve.py            | 51 ++------------------
 src/diffpy/labpdfproc/functions.py           | 51 ++++++++++++--------
 src/diffpy/labpdfproc/labpdfprocapp.py       | 16 ++----
 src/diffpy/labpdfproc/tests/test_fast_cve.py | 48 ------------------
 4 files changed, 39 insertions(+), 127 deletions(-)
 delete mode 100644 src/diffpy/labpdfproc/tests/test_fast_cve.py

diff --git a/src/diffpy/labpdfproc/fast_cve.py b/src/diffpy/labpdfproc/fast_cve.py
index dedc48c..2c1bc09 100644
--- a/src/diffpy/labpdfproc/fast_cve.py
+++ b/src/diffpy/labpdfproc/fast_cve.py
@@ -4,9 +4,7 @@
 import pandas as pd
 from scipy.interpolate import interp1d
 
-from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
-
-TTH_GRID = np.arange(1, 180.1, 0.1)
+FAST_TTH_GRID = np.arange(1, 180.1, 0.1)
 MUD_LIST = [0.5, 1, 2, 3, 4, 5, 6]
 CWD = os.path.dirname(os.path.abspath(__file__))
 INVERSE_CVE_DATA = np.loadtxt(CWD + "/data/inverse_cve.xy")
@@ -14,22 +12,18 @@
 INTERPOLATION_FUNCTIONS = [interp1d(MUD_LIST, coefficients, kind="quadratic") for coefficients in COEFFICIENT_LIST]
 
 
-def fast_compute_cve(diffraction_data, mud, wavelength):
+def fast_compute_cve(mud):
     """
-    use precomputed datasets to compute the cve for given diffraction data, mud and wavelength
+    use precomputed datasets to compute the cve for given mud
 
     Parameters
     ----------
-    diffraction_data Diffraction_object
-      the diffraction pattern
     mud float
       the mu*D of the diffraction object, where D is the diameter of the circle
-    wavelength float
-      the wavelength of the diffraction object
 
     Returns
     -------
-    the diffraction object with cve curves
+    the array of tth grid and the corresponding cve
     """
 
     coefficient_a, coefficient_b, coefficient_c, coefficient_d, coefficient_e = [
@@ -43,39 +37,4 @@ def fast_compute_cve(diffraction_data, mud, wavelength):
         + coefficient_e
     )
     cve = 1 / np.array(inverse_cve)
-
-    orig_grid = diffraction_data.on_tth[0]
-    newcve = np.interp(orig_grid, TTH_GRID, cve)
-    abdo = Diffraction_object(wavelength=wavelength)
-    abdo.insert_scattering_quantity(
-        orig_grid,
-        newcve,
-        "tth",
-        metadata=diffraction_data.metadata,
-        name=f"absorption correction, cve, for {diffraction_data.name}",
-        wavelength=diffraction_data.wavelength,
-        scat_quantity="cve",
-    )
-
-    return abdo
-
-
-def apply_fast_corr(diffraction_pattern, absorption_correction):
-    """
-    Apply absorption correction to the given diffraction object modo with the correction diffraction object abdo
-
-    Parameters
-    ----------
-    diffraction_pattern Diffraction_object
-      the input diffraction object to which the cve will be applied
-    absorption_correction Diffraction_object
-      the diffraction object that contains the cve to be applied
-
-    Returns
-    -------
-    a corrected diffraction object with the correction applied through multiplication
-
-    """
-
-    corrected_pattern = diffraction_pattern * absorption_correction
-    return corrected_pattern
+    return FAST_TTH_GRID, cve
diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index 494be9b..a46bf2c 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 
+from diffpy.labpdfproc.fast_cve import fast_compute_cve
 from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
 
 RADIUS_MM = 1
@@ -27,7 +28,7 @@ def _get_grid_points(self):
         self.grid = {(x, y) for x in xs for y in ys if x**2 + y**2 <= self.radius**2}
         self.total_points_in_grid = len(self.grid)
 
-    # def get_coordinate_index(self, coordinate):  # I think we probably dont need this function?
+    # def get_coordinate_index(self, coordinate):
     #     count = 0
     #     for i, target in enumerate(self.grid):
     #         if coordinate == target:
@@ -172,9 +173,9 @@ def get_path_length(self, grid_point, angle):
         return total_distance, primary_distance, secondary_distance
 
 
-def compute_cve(diffraction_data, mud, wavelength):
+def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
     """
-    compute the cve for given diffraction data, mud and wavelength
+    compute the cve for given diffraction data, mud and wavelength, and a boolean to determine the way to compute
 
     Parameters
     ----------
@@ -185,31 +186,41 @@ def compute_cve(diffraction_data, mud, wavelength):
     wavelength float
       the wavelength of the diffraction object
 
-    Returns
-    -------
-    the diffraction object with cve curves
-
-    it is computed as follows:
+    the brute-force method is computed as follows:
     We first resample data and absorption correction to a more reasonable grid,
     then calculate corresponding cve for the given mud in the resample grid
     (since the same mu*D yields the same cve, we can assume that D/2=1, so mu=mud/2),
     and finally interpolate cve to the original grid in diffraction_data.
+
+    Returns
+    -------
+    the diffraction object with cve curves
+
     """
 
-    mu_sample_invmm = mud / 2
-    abs_correction = Gridded_circle(mu=mu_sample_invmm)
-    distances, muls = [], []
-    for angle in TTH_GRID:
-        abs_correction.set_distances_at_angle(angle)
-        abs_correction.set_muls_at_angle(angle)
-        distances.append(sum(abs_correction.distances))
-        muls.append(sum(abs_correction.muls))
-    distances = np.array(distances) / abs_correction.total_points_in_grid
-    muls = np.array(muls) / abs_correction.total_points_in_grid
-    cve = 1 / muls
+    if brute_force:
+        tth_grid = TTH_GRID
+        mu_sample_invmm = mud / 2
+        abs_correction = Gridded_circle(mu=mu_sample_invmm)
+        distances, muls = [], []
+        for angle in TTH_GRID:
+            abs_correction.set_distances_at_angle(angle)
+            abs_correction.set_muls_at_angle(angle)
+            distances.append(sum(abs_correction.distances))
+            muls.append(sum(abs_correction.muls))
+        distances = np.array(distances) / abs_correction.total_points_in_grid
+        muls = np.array(muls) / abs_correction.total_points_in_grid
+        cve = 1 / muls
+    else:
+        if mud > 6 or mud < 0.5:
+            raise ValueError(
+                "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
+                "Please rerun with a value within this range or use -b to enable brute-force calculation. "
+            )
+        tth_grid, cve = fast_compute_cve(mud)
 
     orig_grid = diffraction_data.on_tth[0]
-    newcve = np.interp(orig_grid, TTH_GRID, cve)
+    newcve = np.interp(orig_grid, tth_grid, cve)
     abdo = Diffraction_object(wavelength=wavelength)
     abdo.insert_scattering_quantity(
         orig_grid,
diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index c2fe16f..24d5b0a 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -1,7 +1,6 @@
 import sys
 from argparse import ArgumentParser
 
-from diffpy.labpdfproc.fast_cve import apply_fast_corr, fast_compute_cve
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
 from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
 from diffpy.utils.parsers.loaddata import loadData
@@ -141,20 +140,11 @@ def main():
             metadata=load_metadata(args, filepath),
         )
 
-        if args.brute_force:
-            absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)
-            corrected_data = apply_corr(input_pattern, absorption_correction)
-        else:
-            if args.mud > 6 or args.mud < 0.5:
-                sys.exit(
-                    "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
-                    "Please rerun with a value within this range or use -b enable brute-force calculation. "
-                )
-            absorption_correction = fast_compute_cve(input_pattern, args.mud, args.wavelength)
-            corrected_data = apply_fast_corr(input_pattern, absorption_correction)
-
+        absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength, args.brute_force)
+        corrected_data = apply_corr(input_pattern, absorption_correction)
         corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
         corrected_data.dump(f"{outfile}", xtype="tth")
+
         if args.output_correction:
             absorption_correction.dump(f"{corrfile}", xtype="tth")
 
diff --git a/src/diffpy/labpdfproc/tests/test_fast_cve.py b/src/diffpy/labpdfproc/tests/test_fast_cve.py
deleted file mode 100644
index 374abe4..0000000
--- a/src/diffpy/labpdfproc/tests/test_fast_cve.py
+++ /dev/null
@@ -1,48 +0,0 @@
-import numpy as np
-
-from diffpy.labpdfproc.fast_cve import apply_fast_corr, fast_compute_cve
-from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
-
-
-def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"):
-    test_do = Diffraction_object(wavelength=1.54)
-    test_do.insert_scattering_quantity(
-        xarray,
-        yarray,
-        "tth",
-        scat_quantity=scat_quantity,
-        name=name,
-        metadata={"thing1": 1, "thing2": "thing2"},
-    )
-    return test_do
-
-
-def test_fast_compute_cve(mocker):
-    xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
-    expected_cve = np.array([0.5, 0.5, 0.5])
-    mocker.patch("numpy.interp", return_value=expected_cve)
-    input_pattern = _instantiate_test_do(xarray, yarray)
-    actual_abdo = fast_compute_cve(input_pattern, mud=1, wavelength=1.54)
-    expected_abdo = _instantiate_test_do(
-        xarray,
-        expected_cve,
-        name="absorption correction, cve, for test",
-        scat_quantity="cve",
-    )
-    assert actual_abdo == expected_abdo
-
-
-def test_apply_fast_corr(mocker):
-    xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
-    expected_cve = np.array([0.5, 0.5, 0.5])
-    mocker.patch("numpy.interp", return_value=expected_cve)
-    input_pattern = _instantiate_test_do(xarray, yarray)
-    absorption_correction = _instantiate_test_do(
-        xarray,
-        expected_cve,
-        name="absorption correction, cve, for test",
-        scat_quantity="cve",
-    )
-    actual_corr = apply_fast_corr(input_pattern, absorption_correction)
-    expected_corr = _instantiate_test_do(xarray, np.array([1, 1, 1]))
-    assert actual_corr == expected_corr

From b7e037e9a68ac65b573795b86f24d3f9f1104ed7 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Fri, 26 Jul 2024 13:21:10 -0400
Subject: [PATCH 06/15] test function for fast_compute_cve

---
 src/diffpy/labpdfproc/tests/test_fast_cve.py | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 src/diffpy/labpdfproc/tests/test_fast_cve.py

diff --git a/src/diffpy/labpdfproc/tests/test_fast_cve.py b/src/diffpy/labpdfproc/tests/test_fast_cve.py
new file mode 100644
index 0000000..9c88335
--- /dev/null
+++ b/src/diffpy/labpdfproc/tests/test_fast_cve.py
@@ -0,0 +1,11 @@
+import numpy as np
+
+from diffpy.labpdfproc.fast_cve import FAST_TTH_GRID, INVERSE_CVE_DATA, fast_compute_cve
+
+
+def test_fast_compute_cve():
+    expected_tth_grid = FAST_TTH_GRID
+    expected_cve = 1 / np.array(INVERSE_CVE_DATA)
+    actual_tth_grid, actual_cve = fast_compute_cve(mud=1)
+    assert np.allclose(actual_tth_grid, expected_tth_grid)
+    assert np.allclose(actual_cve, expected_cve, rtol=1e-5)

From a450dda45b602cf24c67437436767a6ccbb92e70 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Fri, 26 Jul 2024 13:26:36 -0400
Subject: [PATCH 07/15] fix misplaced docstring

---
 src/diffpy/labpdfproc/tools.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index 5ada419..c56aa30 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -17,15 +17,15 @@ def set_output_directory(args):
     args argparse.Namespace
         the arguments from the parser
 
-    Returns
-    -------
-    pathlib.PosixPath that contains the full path of the output directory
-
     it is determined as follows:
     If user provides an output directory, use it.
     Otherwise, we set it to the current directory if nothing is provided.
     We then create the directory if it does not exist.
 
+    Returns
+    -------
+    pathlib.PosixPath that contains the full path of the output directory
+
     """
     output_dir = Path(args.output_directory).resolve() if args.output_directory else Path.cwd().resolve()
     output_dir.mkdir(parents=True, exist_ok=True)
@@ -110,13 +110,13 @@ def set_wavelength(args):
     args argparse.Namespace
         the arguments from the parser
 
+    we raise an ValueError if the input wavelength is non-positive
+    or if the input anode_type is not one of the known sources
+
     Returns
     -------
     args argparse.Namespace
 
-    we raise an ValueError if the input wavelength is non-positive
-    or if the input anode_type is not one of the known sources
-
     """
     if args.wavelength is not None and args.wavelength <= 0:
         raise ValueError(

From fc4d87649a325aa6dddd31fbb2f0e62843b49255 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Mon, 29 Jul 2024 13:06:04 -0400
Subject: [PATCH 08/15] integrate fast cve module in functions

---
 src/diffpy/labpdfproc/fast_cve.py            | 40 --------------------
 src/diffpy/labpdfproc/functions.py           | 22 ++++++++---
 src/diffpy/labpdfproc/tests/test_fast_cve.py | 11 ------
 3 files changed, 17 insertions(+), 56 deletions(-)
 delete mode 100644 src/diffpy/labpdfproc/fast_cve.py
 delete mode 100644 src/diffpy/labpdfproc/tests/test_fast_cve.py

diff --git a/src/diffpy/labpdfproc/fast_cve.py b/src/diffpy/labpdfproc/fast_cve.py
deleted file mode 100644
index 2c1bc09..0000000
--- a/src/diffpy/labpdfproc/fast_cve.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import os
-
-import numpy as np
-import pandas as pd
-from scipy.interpolate import interp1d
-
-FAST_TTH_GRID = np.arange(1, 180.1, 0.1)
-MUD_LIST = [0.5, 1, 2, 3, 4, 5, 6]
-CWD = os.path.dirname(os.path.abspath(__file__))
-INVERSE_CVE_DATA = np.loadtxt(CWD + "/data/inverse_cve.xy")
-COEFFICIENT_LIST = np.array(pd.read_csv(CWD + "/data/coefficient_list.csv", header=None))
-INTERPOLATION_FUNCTIONS = [interp1d(MUD_LIST, coefficients, kind="quadratic") for coefficients in COEFFICIENT_LIST]
-
-
-def fast_compute_cve(mud):
-    """
-    use precomputed datasets to compute the cve for given mud
-
-    Parameters
-    ----------
-    mud float
-      the mu*D of the diffraction object, where D is the diameter of the circle
-
-    Returns
-    -------
-    the array of tth grid and the corresponding cve
-    """
-
-    coefficient_a, coefficient_b, coefficient_c, coefficient_d, coefficient_e = [
-        interpolation_function(mud) for interpolation_function in INTERPOLATION_FUNCTIONS
-    ]
-    inverse_cve = (
-        coefficient_a * INVERSE_CVE_DATA**4
-        + coefficient_b * INVERSE_CVE_DATA**3
-        + coefficient_c * INVERSE_CVE_DATA**2
-        + coefficient_d * INVERSE_CVE_DATA**1
-        + coefficient_e
-    )
-    cve = 1 / np.array(inverse_cve)
-    return FAST_TTH_GRID, cve
diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index a46bf2c..254a1fe 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -1,13 +1,22 @@
 import math
+import os
 
 import numpy as np
+import pandas as pd
+from scipy.interpolate import interp1d
 
-from diffpy.labpdfproc.fast_cve import fast_compute_cve
 from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
 
 RADIUS_MM = 1
 N_POINTS_ON_DIAMETER = 300
-TTH_GRID = np.arange(1, 141, 1)
+TTH_GRID = np.arange(1, 180.1, 0.1)
+
+# pre-computed datasets for fast calculation
+MUD_LIST = [0.5, 1, 2, 3, 4, 5, 6]
+CWD = os.path.dirname(os.path.abspath(__file__))
+MULS = np.loadtxt(CWD + "/data/inverse_cve.xy")
+COEFFICIENT_LIST = np.array(pd.read_csv(CWD + "/data/coefficient_list.csv", header=None))
+INTERPOLATION_FUNCTIONS = [interp1d(MUD_LIST, coefficients, kind="quadratic") for coefficients in COEFFICIENT_LIST]
 
 
 class Gridded_circle:
@@ -199,7 +208,6 @@ def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
     """
 
     if brute_force:
-        tth_grid = TTH_GRID
         mu_sample_invmm = mud / 2
         abs_correction = Gridded_circle(mu=mu_sample_invmm)
         distances, muls = [], []
@@ -217,10 +225,14 @@ def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
                 "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
                 "Please rerun with a value within this range or use -b to enable brute-force calculation. "
             )
-        tth_grid, cve = fast_compute_cve(mud)
+        coeff_a, coeff_b, coeff_c, coeff_d, coeff_e = [
+            interpolation_function(mud) for interpolation_function in INTERPOLATION_FUNCTIONS
+        ]
+        muls = np.array(coeff_a * MULS**4 + coeff_b * MULS**3 + coeff_c * MULS**2 + coeff_d * MULS + coeff_e)
+        cve = 1 / muls
 
     orig_grid = diffraction_data.on_tth[0]
-    newcve = np.interp(orig_grid, tth_grid, cve)
+    newcve = np.interp(orig_grid, TTH_GRID, cve)
     abdo = Diffraction_object(wavelength=wavelength)
     abdo.insert_scattering_quantity(
         orig_grid,
diff --git a/src/diffpy/labpdfproc/tests/test_fast_cve.py b/src/diffpy/labpdfproc/tests/test_fast_cve.py
deleted file mode 100644
index 9c88335..0000000
--- a/src/diffpy/labpdfproc/tests/test_fast_cve.py
+++ /dev/null
@@ -1,11 +0,0 @@
-import numpy as np
-
-from diffpy.labpdfproc.fast_cve import FAST_TTH_GRID, INVERSE_CVE_DATA, fast_compute_cve
-
-
-def test_fast_compute_cve():
-    expected_tth_grid = FAST_TTH_GRID
-    expected_cve = 1 / np.array(INVERSE_CVE_DATA)
-    actual_tth_grid, actual_cve = fast_compute_cve(mud=1)
-    assert np.allclose(actual_tth_grid, expected_tth_grid)
-    assert np.allclose(actual_cve, expected_cve, rtol=1e-5)

From 956408d606351252c8b52b2056d0b2cadff8b30f Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 22 Aug 2024 19:30:55 -0400
Subject: [PATCH 09/15] add private function _cve_method in compute_cve to
 select cve computers _cve_brute_force or _cve_interp_polynomial

---
 src/diffpy/labpdfproc/functions.py | 97 +++++++++++++++++-------------
 1 file changed, 55 insertions(+), 42 deletions(-)

diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index 254a1fe..55547b8 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -37,16 +37,6 @@ def _get_grid_points(self):
         self.grid = {(x, y) for x in xs for y in ys if x**2 + y**2 <= self.radius**2}
         self.total_points_in_grid = len(self.grid)
 
-    # def get_coordinate_index(self, coordinate):
-    #     count = 0
-    #     for i, target in enumerate(self.grid):
-    #         if coordinate == target:
-    #             return i
-    #         else:
-    #             count += 1
-    #     if count >= len(self.grid):
-    #         raise IndexError(f"WARNING: no coordinate {coordinate} found in coordinates list")
-
     def set_distances_at_angle(self, angle):
         """
         given an angle, set the distances from the grid points to the entry and exit coordinates
@@ -182,9 +172,62 @@ def get_path_length(self, grid_point, angle):
         return total_distance, primary_distance, secondary_distance
 
 
+def _cve_brute_force(diffraction_data, mud, wavelength):
+    """
+    compute cve using brute-force method
+
+    it is computed as follows:
+    We first resample data and absorption correction to a more reasonable grid,
+    then calculate corresponding cve for the given mud in the resample grid
+    (since the same mu*D yields the same cve, we can assume that D/2=1, so mu=mud/2),
+    and finally interpolate cve to the original grid in diffraction_data.
+    """
+
+    mu_sample_invmm = mud / 2
+    abs_correction = Gridded_circle(mu=mu_sample_invmm)
+    distances, muls = [], []
+    for angle in TTH_GRID:
+        abs_correction.set_distances_at_angle(angle)
+        abs_correction.set_muls_at_angle(angle)
+        distances.append(sum(abs_correction.distances))
+        muls.append(sum(abs_correction.muls))
+    distances = np.array(distances) / abs_correction.total_points_in_grid
+    muls = np.array(muls) / abs_correction.total_points_in_grid
+    cve = 1 / muls
+    return cve
+
+
+def _cve_interp_polynomial(diffraction_data, mud, wavelength):
+    """
+    compute cve using polynomial interpolation method, raise an error if mu*D is out of the range (0.5 to 6)
+    """
+
+    if mud > 6 or mud < 0.5:
+        raise ValueError(
+            "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
+            "Please rerun with a value within this range or use -b to enable brute-force calculation. "
+        )
+    coeff_a, coeff_b, coeff_c, coeff_d, coeff_e = [
+        interpolation_function(mud) for interpolation_function in INTERPOLATION_FUNCTIONS
+    ]
+    muls = np.array(coeff_a * MULS**4 + coeff_b * MULS**3 + coeff_c * MULS**2 + coeff_d * MULS + coeff_e)
+    cve = 1 / muls
+    return cve
+
+
+def _cve_method(diffraction_data, mud, wavelength, brute_force=False):
+    """
+    selects the appropriate CVE calculation method
+    """
+    if brute_force:
+        return _cve_brute_force(diffraction_data, mud, wavelength)
+    else:
+        return _cve_interp_polynomial(diffraction_data, mud, wavelength)
+
+
 def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
     """
-    compute the cve for given diffraction data, mud and wavelength, and a boolean to determine the way to compute
+    compute the cve for given diffraction data, mud, and wavelength, using the selected method
 
     Parameters
     ----------
@@ -195,42 +238,13 @@ def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
     wavelength float
       the wavelength of the diffraction object
 
-    the brute-force method is computed as follows:
-    We first resample data and absorption correction to a more reasonable grid,
-    then calculate corresponding cve for the given mud in the resample grid
-    (since the same mu*D yields the same cve, we can assume that D/2=1, so mu=mud/2),
-    and finally interpolate cve to the original grid in diffraction_data.
-
     Returns
     -------
     the diffraction object with cve curves
 
     """
 
-    if brute_force:
-        mu_sample_invmm = mud / 2
-        abs_correction = Gridded_circle(mu=mu_sample_invmm)
-        distances, muls = [], []
-        for angle in TTH_GRID:
-            abs_correction.set_distances_at_angle(angle)
-            abs_correction.set_muls_at_angle(angle)
-            distances.append(sum(abs_correction.distances))
-            muls.append(sum(abs_correction.muls))
-        distances = np.array(distances) / abs_correction.total_points_in_grid
-        muls = np.array(muls) / abs_correction.total_points_in_grid
-        cve = 1 / muls
-    else:
-        if mud > 6 or mud < 0.5:
-            raise ValueError(
-                "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
-                "Please rerun with a value within this range or use -b to enable brute-force calculation. "
-            )
-        coeff_a, coeff_b, coeff_c, coeff_d, coeff_e = [
-            interpolation_function(mud) for interpolation_function in INTERPOLATION_FUNCTIONS
-        ]
-        muls = np.array(coeff_a * MULS**4 + coeff_b * MULS**3 + coeff_c * MULS**2 + coeff_d * MULS + coeff_e)
-        cve = 1 / muls
-
+    cve = _cve_method(diffraction_data, mud, wavelength, brute_force)
     orig_grid = diffraction_data.on_tth[0]
     newcve = np.interp(orig_grid, TTH_GRID, cve)
     abdo = Diffraction_object(wavelength=wavelength)
@@ -243,7 +257,6 @@ def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
         wavelength=diffraction_data.wavelength,
         scat_quantity="cve",
     )
-
     return abdo
 
 

From 4bbe4a2b88fc8782bf19bfd8c00f4cce13e563b9 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Mon, 26 Aug 2024 15:38:22 -0400
Subject: [PATCH 10/15] add method to argparser and correct functions and
 docstrings

---
 src/diffpy/labpdfproc/functions.py            | 39 +++++++++----------
 src/diffpy/labpdfproc/labpdfprocapp.py        | 16 ++++----
 src/diffpy/labpdfproc/tests/test_functions.py |  6 +--
 3 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index 55547b8..a355f87 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -10,6 +10,7 @@
 RADIUS_MM = 1
 N_POINTS_ON_DIAMETER = 300
 TTH_GRID = np.arange(1, 180.1, 0.1)
+CVE_METHODS = ["brute_force", "polynomial_interpolation"]
 
 # pre-computed datasets for fast calculation
 MUD_LIST = [0.5, 1, 2, 3, 4, 5, 6]
@@ -172,15 +173,10 @@ def get_path_length(self, grid_point, angle):
         return total_distance, primary_distance, secondary_distance
 
 
-def _cve_brute_force(diffraction_data, mud, wavelength):
+def _cve_brute_force(mud):
     """
-    compute cve using brute-force method
-
-    it is computed as follows:
-    We first resample data and absorption correction to a more reasonable grid,
-    then calculate corresponding cve for the given mud in the resample grid
-    (since the same mu*D yields the same cve, we can assume that D/2=1, so mu=mud/2),
-    and finally interpolate cve to the original grid in diffraction_data.
+    compute cve for the given mud on a global grid using the brute-force method
+    assume mu=mud/2, given that the same mu*D yields the same cve and D/2=1
     """
 
     mu_sample_invmm = mud / 2
@@ -197,15 +193,15 @@ def _cve_brute_force(diffraction_data, mud, wavelength):
     return cve
 
 
-def _cve_interp_polynomial(diffraction_data, mud, wavelength):
+def _cve_polynomial_interpolation(mud):
     """
     compute cve using polynomial interpolation method, raise an error if mu*D is out of the range (0.5 to 6)
     """
 
     if mud > 6 or mud < 0.5:
         raise ValueError(
-            "mu*D is out of the acceptable range (0.5 to 6) for fast calculation. "
-            "Please rerun with a value within this range or use -b to enable brute-force calculation. "
+            f"mu*D is out of the acceptable range (0.5 to 6) for polynomial interpolation. "
+            f"Please rerun with a value within this range or specifying another method from {* CVE_METHODS, }."
         )
     coeff_a, coeff_b, coeff_c, coeff_d, coeff_e = [
         interpolation_function(mud) for interpolation_function in INTERPOLATION_FUNCTIONS
@@ -215,19 +211,20 @@ def _cve_interp_polynomial(diffraction_data, mud, wavelength):
     return cve
 
 
-def _cve_method(diffraction_data, mud, wavelength, brute_force=False):
+def _compute_cve(method, mud):
     """
-    selects the appropriate CVE calculation method
+    compute cve for the given mud on a global grid using the specified method
     """
-    if brute_force:
-        return _cve_brute_force(diffraction_data, mud, wavelength)
-    else:
-        return _cve_interp_polynomial(diffraction_data, mud, wavelength)
+    methods = {
+        "brute_force": _cve_brute_force,
+        "polynomial_interpolation": _cve_polynomial_interpolation,
+    }
+    return methods[method](mud)
 
 
-def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
+def interpolate_cve(diffraction_data, mud, wavelength, method="polynomial_interpolation"):
     """
-    compute the cve for given diffraction data, mud, and wavelength, using the selected method
+    compute and interpolate the cve for the given diffraction data, mud, and wavelength, using the selected method
 
     Parameters
     ----------
@@ -237,6 +234,8 @@ def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
       the mu*D of the diffraction object, where D is the diameter of the circle
     wavelength float
       the wavelength of the diffraction object
+    method str
+      the method used to calculate cve
 
     Returns
     -------
@@ -244,7 +243,7 @@ def compute_cve(diffraction_data, mud, wavelength, brute_force=False):
 
     """
 
-    cve = _cve_method(diffraction_data, mud, wavelength, brute_force)
+    cve = _compute_cve(method, mud)
     orig_grid = diffraction_data.on_tth[0]
     newcve = np.interp(orig_grid, TTH_GRID, cve)
     abdo = Diffraction_object(wavelength=wavelength)
diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 24d5b0a..0d25c54 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -1,7 +1,7 @@
 import sys
 from argparse import ArgumentParser
 
-from diffpy.labpdfproc.functions import apply_corr, compute_cve
+from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, interpolate_cve
 from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
@@ -45,7 +45,7 @@ def get_args(override_cli_inputs=None):
         "-o",
         "--output-directory",
         help="The name of the output directory. If not specified "
-        "then corrected files will be written to the current directory."
+        "then corrected files will be written to the current directory. "
         "If the specified directory doesn't exist it will be created.",
         default=None,
     )
@@ -72,11 +72,11 @@ def get_args(override_cli_inputs=None):
         help="Outputs will not overwrite existing file unless --force is specified.",
     )
     p.add_argument(
-        "-b",
-        "--brute-force",
-        action="store_true",
-        help="The absorption correction will be computed using brute-force calculation "
-        "if this flag is set. Default is using fast calculation. ",
+        "-m",
+        "--method",
+        help=f"The method for computing absorption correction. Allowed methods: {*CVE_METHODS, }. "
+        f"Default method is polynomial interpolation if not specified. ",
+        default="polynomial_interpolation",
     )
     p.add_argument(
         "-u",
@@ -140,7 +140,7 @@ def main():
             metadata=load_metadata(args, filepath),
         )
 
-        absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength, args.brute_force)
+        absorption_correction = interpolate_cve(input_pattern, args.mud, args.wavelength, args.method)
         corrected_data = apply_corr(input_pattern, absorption_correction)
         corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
         corrected_data.dump(f"{outfile}", xtype="tth")
diff --git a/src/diffpy/labpdfproc/tests/test_functions.py b/src/diffpy/labpdfproc/tests/test_functions.py
index 75ef019..19acd64 100644
--- a/src/diffpy/labpdfproc/tests/test_functions.py
+++ b/src/diffpy/labpdfproc/tests/test_functions.py
@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from diffpy.labpdfproc.functions import Gridded_circle, apply_corr, compute_cve
+from diffpy.labpdfproc.functions import Gridded_circle, apply_corr, interpolate_cve
 from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
 
 params1 = [
@@ -69,13 +69,13 @@ def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"):
     return test_do
 
 
-def test_compute_cve(mocker):
+def test_interpolate_cve(mocker):
     xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
     expected_cve = np.array([0.5, 0.5, 0.5])
     mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", xarray)
     mocker.patch("numpy.interp", return_value=expected_cve)
     input_pattern = _instantiate_test_do(xarray, yarray)
-    actual_abdo = compute_cve(input_pattern, mud=1, wavelength=1.54)
+    actual_abdo = interpolate_cve(input_pattern, mud=1, wavelength=1.54)
     expected_abdo = _instantiate_test_do(
         xarray,
         expected_cve,

From b91b6ecc8163f79e445f29d0820688a4563deba6 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Mon, 26 Aug 2024 15:41:10 -0400
Subject: [PATCH 11/15] change cwd path from os to pathlib

---
 src/diffpy/labpdfproc/functions.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index a355f87..c10a92e 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -1,5 +1,5 @@
 import math
-import os
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -12,11 +12,11 @@
 TTH_GRID = np.arange(1, 180.1, 0.1)
 CVE_METHODS = ["brute_force", "polynomial_interpolation"]
 
-# pre-computed datasets for fast calculation
+# pre-computed datasets for polynomial interpolation (fast calculation)
 MUD_LIST = [0.5, 1, 2, 3, 4, 5, 6]
-CWD = os.path.dirname(os.path.abspath(__file__))
-MULS = np.loadtxt(CWD + "/data/inverse_cve.xy")
-COEFFICIENT_LIST = np.array(pd.read_csv(CWD + "/data/coefficient_list.csv", header=None))
+CWD = Path(__file__).parent.resolve()
+MULS = np.loadtxt(CWD / "data" / "inverse_cve.xy")
+COEFFICIENT_LIST = np.array(pd.read_csv(CWD / "data" / "coefficient_list.csv", header=None))
 INTERPOLATION_FUNCTIONS = [interp1d(MUD_LIST, coefficients, kind="quadratic") for coefficients in COEFFICIENT_LIST]
 
 

From e7d3d0591b28f0b128899f9e90bb64f0561f55d9 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Mon, 26 Aug 2024 15:45:15 -0400
Subject: [PATCH 12/15] add method argument to metadata test

---
 src/diffpy/labpdfproc/tests/test_tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index fda91fb..e17ed42 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -312,7 +312,7 @@ def test_load_metadata(mocker, user_filesystem):
             "wavelength": 0.71,
             "output_directory": str(Path.cwd().resolve()),
             "xtype": "tth",
-            "brute_force": False,
+            "method": "polynomial_interpolation",
             "key": "value",
             "username": "cli_username",
             "email": "cli@email.com",

From bb28204a10d2a778e2001a66f713c9317cf18417 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Wed, 28 Aug 2024 11:04:21 -0400
Subject: [PATCH 13/15] change compute cve function to call cve methods and
 interpolate tth

---
 src/diffpy/labpdfproc/functions.py            | 13 ++++++++-----
 src/diffpy/labpdfproc/labpdfprocapp.py        |  4 ++--
 src/diffpy/labpdfproc/tests/test_functions.py |  6 +++---
 3 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index c10a92e..d136926 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -211,18 +211,20 @@ def _cve_polynomial_interpolation(mud):
     return cve
 
 
-def _compute_cve(method, mud):
+def _cve_method(method):
     """
-    compute cve for the given mud on a global grid using the specified method
+    retrieve the cve computation function for the given method
     """
     methods = {
         "brute_force": _cve_brute_force,
         "polynomial_interpolation": _cve_polynomial_interpolation,
     }
-    return methods[method](mud)
+    if method not in CVE_METHODS:
+        raise ValueError(f"Unknown method: {method}. Allowed methods are {*CVE_METHODS, }.")
+    return methods[method]
 
 
-def interpolate_cve(diffraction_data, mud, wavelength, method="polynomial_interpolation"):
+def compute_cve(diffraction_data, mud, wavelength, method="polynomial_interpolation"):
     """
     compute and interpolate the cve for the given diffraction data, mud, and wavelength, using the selected method
 
@@ -243,7 +245,8 @@ def interpolate_cve(diffraction_data, mud, wavelength, method="polynomial_interp
 
     """
 
-    cve = _compute_cve(method, mud)
+    cve_function = _cve_method(method)
+    cve = cve_function(mud)
     orig_grid = diffraction_data.on_tth[0]
     newcve = np.interp(orig_grid, TTH_GRID, cve)
     abdo = Diffraction_object(wavelength=wavelength)
diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 0d25c54..2c21605 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -1,7 +1,7 @@
 import sys
 from argparse import ArgumentParser
 
-from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, interpolate_cve
+from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, compute_cve
 from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
@@ -140,7 +140,7 @@ def main():
             metadata=load_metadata(args, filepath),
         )
 
-        absorption_correction = interpolate_cve(input_pattern, args.mud, args.wavelength, args.method)
+        absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength, args.method)
         corrected_data = apply_corr(input_pattern, absorption_correction)
         corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
         corrected_data.dump(f"{outfile}", xtype="tth")
diff --git a/src/diffpy/labpdfproc/tests/test_functions.py b/src/diffpy/labpdfproc/tests/test_functions.py
index 19acd64..75ef019 100644
--- a/src/diffpy/labpdfproc/tests/test_functions.py
+++ b/src/diffpy/labpdfproc/tests/test_functions.py
@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from diffpy.labpdfproc.functions import Gridded_circle, apply_corr, interpolate_cve
+from diffpy.labpdfproc.functions import Gridded_circle, apply_corr, compute_cve
 from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
 
 params1 = [
@@ -69,13 +69,13 @@ def _instantiate_test_do(xarray, yarray, name="test", scat_quantity="x-ray"):
     return test_do
 
 
-def test_interpolate_cve(mocker):
+def test_compute_cve(mocker):
     xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
     expected_cve = np.array([0.5, 0.5, 0.5])
     mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", xarray)
     mocker.patch("numpy.interp", return_value=expected_cve)
     input_pattern = _instantiate_test_do(xarray, yarray)
-    actual_abdo = interpolate_cve(input_pattern, mud=1, wavelength=1.54)
+    actual_abdo = compute_cve(input_pattern, mud=1, wavelength=1.54)
     expected_abdo = _instantiate_test_do(
         xarray,
         expected_cve,

From 3c6b1281fa55c72de119940459fc0679de30620b Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Wed, 28 Aug 2024 14:36:56 -0400
Subject: [PATCH 14/15] updated compute_cve to use DOs consistently

---
 src/diffpy/labpdfproc/functions.py            | 44 ++++++++++++++-----
 src/diffpy/labpdfproc/labpdfprocapp.py        |  2 +-
 src/diffpy/labpdfproc/tests/test_functions.py |  2 +-
 3 files changed, 35 insertions(+), 13 deletions(-)

diff --git a/src/diffpy/labpdfproc/functions.py b/src/diffpy/labpdfproc/functions.py
index d136926..6d80a4d 100644
--- a/src/diffpy/labpdfproc/functions.py
+++ b/src/diffpy/labpdfproc/functions.py
@@ -173,7 +173,7 @@ def get_path_length(self, grid_point, angle):
         return total_distance, primary_distance, secondary_distance
 
 
-def _cve_brute_force(mud):
+def _cve_brute_force(diffraction_data, mud):
     """
     compute cve for the given mud on a global grid using the brute-force method
     assume mu=mud/2, given that the same mu*D yields the same cve and D/2=1
@@ -190,10 +190,21 @@ def _cve_brute_force(mud):
     distances = np.array(distances) / abs_correction.total_points_in_grid
     muls = np.array(muls) / abs_correction.total_points_in_grid
     cve = 1 / muls
-    return cve
+
+    abdo = Diffraction_object(wavelength=diffraction_data.wavelength)
+    abdo.insert_scattering_quantity(
+        TTH_GRID,
+        cve,
+        "tth",
+        metadata=diffraction_data.metadata,
+        name=f"absorption correction, cve, for {diffraction_data.name}",
+        wavelength=diffraction_data.wavelength,
+        scat_quantity="cve",
+    )
+    return abdo
 
 
-def _cve_polynomial_interpolation(mud):
+def _cve_polynomial_interpolation(diffraction_data, mud):
     """
     compute cve using polynomial interpolation method, raise an error if mu*D is out of the range (0.5 to 6)
     """
@@ -208,7 +219,18 @@ def _cve_polynomial_interpolation(mud):
     ]
     muls = np.array(coeff_a * MULS**4 + coeff_b * MULS**3 + coeff_c * MULS**2 + coeff_d * MULS + coeff_e)
     cve = 1 / muls
-    return cve
+
+    abdo = Diffraction_object(wavelength=diffraction_data.wavelength)
+    abdo.insert_scattering_quantity(
+        TTH_GRID,
+        cve,
+        "tth",
+        metadata=diffraction_data.metadata,
+        name=f"absorption correction, cve, for {diffraction_data.name}",
+        wavelength=diffraction_data.wavelength,
+        scat_quantity="cve",
+    )
+    return abdo
 
 
 def _cve_method(method):
@@ -224,9 +246,9 @@ def _cve_method(method):
     return methods[method]
 
 
-def compute_cve(diffraction_data, mud, wavelength, method="polynomial_interpolation"):
+def compute_cve(diffraction_data, mud, method="polynomial_interpolation"):
     """
-    compute and interpolate the cve for the given diffraction data, mud, and wavelength, using the selected method
+    compute and interpolate the cve for the given diffraction data and mud using the selected method
 
     Parameters
     ----------
@@ -234,8 +256,6 @@ def compute_cve(diffraction_data, mud, wavelength, method="polynomial_interpolat
       the diffraction pattern
     mud float
       the mu*D of the diffraction object, where D is the diameter of the circle
-    wavelength float
-      the wavelength of the diffraction object
     method str
       the method used to calculate cve
 
@@ -246,10 +266,12 @@ def compute_cve(diffraction_data, mud, wavelength, method="polynomial_interpolat
     """
 
     cve_function = _cve_method(method)
-    cve = cve_function(mud)
+    abdo_on_global_tth = cve_function(diffraction_data, mud)
+    global_tth = abdo_on_global_tth.on_tth[0]
+    cve_on_global_tth = abdo_on_global_tth.on_tth[1]
     orig_grid = diffraction_data.on_tth[0]
-    newcve = np.interp(orig_grid, TTH_GRID, cve)
-    abdo = Diffraction_object(wavelength=wavelength)
+    newcve = np.interp(orig_grid, global_tth, cve_on_global_tth)
+    abdo = Diffraction_object(wavelength=diffraction_data.wavelength)
     abdo.insert_scattering_quantity(
         orig_grid,
         newcve,
diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 2c21605..9510e90 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -140,7 +140,7 @@ def main():
             metadata=load_metadata(args, filepath),
         )
 
-        absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength, args.method)
+        absorption_correction = compute_cve(input_pattern, args.mud, args.method)
         corrected_data = apply_corr(input_pattern, absorption_correction)
         corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
         corrected_data.dump(f"{outfile}", xtype="tth")
diff --git a/src/diffpy/labpdfproc/tests/test_functions.py b/src/diffpy/labpdfproc/tests/test_functions.py
index 75ef019..417a34f 100644
--- a/src/diffpy/labpdfproc/tests/test_functions.py
+++ b/src/diffpy/labpdfproc/tests/test_functions.py
@@ -75,7 +75,7 @@ def test_compute_cve(mocker):
     mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", xarray)
     mocker.patch("numpy.interp", return_value=expected_cve)
     input_pattern = _instantiate_test_do(xarray, yarray)
-    actual_abdo = compute_cve(input_pattern, mud=1, wavelength=1.54)
+    actual_abdo = compute_cve(input_pattern, mud=1)
     expected_abdo = _instantiate_test_do(
         xarray,
         expected_cve,

From 377607a4334935e65f0888a7aee62af2bb9234b2 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Wed, 28 Aug 2024 14:39:44 -0400
Subject: [PATCH 15/15] change output file format from .chi to .xy

---
 src/diffpy/labpdfproc/labpdfprocapp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 9510e90..9325f20 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -115,8 +115,8 @@ def main():
     for filepath in args.input_paths:
         outfilestem = filepath.stem + "_corrected"
         corrfilestem = filepath.stem + "_cve"
-        outfile = args.output_directory / (outfilestem + ".chi")
-        corrfile = args.output_directory / (corrfilestem + ".chi")
+        outfile = args.output_directory / (outfilestem + ".xy")
+        corrfile = args.output_directory / (corrfilestem + ".xy")
 
         if outfile.exists() and not args.force_overwrite:
             sys.exit(